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Background and Introduction: Over the last decade, treatment of patients with advanced non-small cell lung cancer (NSCLC) has become dependent on tissue and/or blood biomarkers to guide treatment decisions. Timely access to comprehensive biomarker and tumor signature information is crucial for diagnostic testing. With the rapid development and implementation of complex biomarker testing, comprehensive molecular profiling with in-depth analysis of DNA, RNA, and proteins can be easily performed. Initial data from the MedStar Health system showed considerable disparities in the use of next generation sequencing (NGS) between hospitals, and there is a clear need to improve education and understanding regarding which cases are appropriate for NGS, as well as the use of protocols to make those decisions in an expeditious manner., Materials and Methods: Clinical pathways are systems-based tools that aim to create greater transparency around care decision making, therapeutic selection, and care delivery. They enhance quality and efficiency by reducing non-value-added intra-provider variability in care. We aimed to create a comprehensive clinical pathway system, the Targetable Molecular Algorithm (TMA), to increase the understanding and use of NGS in NSCLC by physicians in training, oncology nurse navigators, nurse practitioners, and general oncologists., Discussion: We provide an overview of the implementation of the platform along with navigation guide. A realistic case study-a typical clinical workflow for a patient requiring NGS testing with an EGFR mutation-is also reviewed, demonstrating how the TMA platform can be applied. Additionally, we highlight the importance of the resource, and discuss its strengths, weaknesses, and potential future applications., Results and Conclusion: This new and innovative pathway system will make decision-making easier for clinicians trying to understand the appropriate tests and treatment algorithms for their patients. Our aim is to increase the appropriate and timely use of NGS among health-system providers with the hope that this system will empower physicians to provide better care by providing a quick, simple, user-friendly tool for comprehensive patient care., Competing Interests: J.R. is Advisory Board/Consultant at Genentech/Roche, Sanofi/Genzyme, Personalis, Guardant, Astrazeneca, BMS, Arcus, Abbvie, Daiichi Sankyo, Catalym. He receives research funding (to institution) from: Genentech/Roche, Verastem, Nuvalent, Mesothelioma Applied Research Foundation, LUNGevity Foundation. He has received honoraria/Speaking Fees from Astrazeneca, Merck. C.K. is Consultant/advisory board member at Novartis, Janssen, AstraZeneca, Sanofi, PierianDx, Diffuse pharmaceuticals, Mirati, Jazz Pharmaceuticals, Arcus Biosciences, Daiichi Sankyo, Eisai, Regeneron. He receives research funding (to institution) from: AstraZeneca, Bristol-Myers Squibb, Novartis, Genentech, Janssen, Regeneron, Debiopharm, Karyopharm, Daiichi-Sankyo, Lyell Immunopharma., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

Although machine learning (ML) has shown promise across disciplines, out-of-sample generalizability is concerning. This is currently addressed by sharing multi-site data, but such centralization is challenging/infeasible to scale due to various limitations. Federated ML (FL) provides an alternative paradigm for accurate and generalizable ML, by only sharing numerical model updates. Here we present the largest FL study to-date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature (n = 6, 314). We demonstrate a 33% delineation improvement for the surgically targetable tumor, and 23% for the complete tumor extent, over a publicly trained model. We anticipate our study to: 1) enable more healthcare studies informed by large diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further analyses for glioblastoma by releasing our consensus model, and 3) demonstrate the FL effectiveness at such scale and task-complexity as a paradigm shift for multi-site collaborations, alleviating the need for data-sharing., (© 2022. The Author(s).)

Malignancy of the brain and CNS is unfortunately a common diagnosis. A large subset of these lesions tends to be high grade tumors which portend poor prognoses and low survival rates, and are estimated to be the tenth leading cause of death worldwide. The complex nature of the brain tissue environment in which these lesions arise offers a rich opportunity for translational research. Magnetic Resonance Imaging (MRI) can provide a comprehensive view of the abnormal regions in the brain, therefore, its applications in the translational brain cancer research is considered essential for the diagnosis and monitoring of disease. Recent years has seen rapid growth in the field of radiogenomics, especially in cancer, and scientists have been able to successfully integrate the quantitative data extracted from medical images (also known as radiomics) with genomics to answer new and clinically relevant questions. In this paper, we took raw MRI scans from the REMBRANDT data collection from public domain, and performed volumetric segmentation to identify subregions of the brain. Radiomic features were then extracted to represent the MRIs in a quantitative yet summarized format. This resulting dataset now enables further biomedical and integrative data analysis, and is being made public via the NeuroImaging Tools & Resources Collaboratory (NITRC) repository ( https://www.nitrc.org/projects/rembrandt_brain/ )., (© 2022. The Author(s).)

Background: Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surface plasmon resonance is a very powerful tool in different stages of small molecule drug development and antibody characterization. Both academic institutions and pharmaceutical industry extensively utilize this method for screening and validation studies involving direct molecular interactions. In most applications of the surface plasmon resonance technology, one of the studied molecules is immobilized on a microchip, while the second molecule is delivered through a microfluidic system over the immobilized molecules. Changes in total mass on the chip surface is recorded in real time as an indicator of the molecular interactions., Main Body: Quality and accuracy of the surface plasmon resonance data depend on experimental variables, including buffer composition, type of sensor chip, coupling chemistry of molecules on the sensor surface, and surface regeneration conditions. These technical details are generally included in materials and methods sections of published manuscripts and are not easily accessible using the common internet browser search engines or PubMed. Herein, we introduce a surface plasmon resonance database, www.sprdatabase.info that contains technical details extracted from 5140 publications with surface plasmon resonance data. We also provide an analysis of experimental conditions preferred by different laboratories. These experimental variables can be searched within the database and help future users of this technology to design better experiments., Conclusion: Amine coupling and CM5 chips were the most common methods used for immobilizing proteins in surface plasmon resonance experiments. However, number of different chips, capture methods and buffer conditions were used by multiple investigators. We predict that the database will significantly help the scientific community using this technology and hope that users will provide feedback to improve and expand the database indefinitely. Publicly available information in the database can save a great amount of time and resources by assisting initial optimization and troubleshooting of surface plasmon resonance experiments.